Merge pull request #36 from EBjerrum/drawing_settings

Drawing settings

Author: EBjerrum

rdeditor/molViewWidget.py

@@ -21,7 +21,7 @@
 
 # The Viewer Class
 class MolWidget(QtSvgWidgets.QSvgWidget):
-    def __init__(self, mol=None, parent=None):
+    def __init__(self, mol=None, parent=None, moldrawoptions: rdMolDraw2D.MolDrawOptions = None):
         # Also init the super class
         super(MolWidget, self).__init__(parent)
 
@@ -49,6 +49,16 @@ def __init__(self, mol=None, parent=None):
         self._sanitize = False
         self._updatepropertycache = False
 
+        # Draw options
+        if moldrawoptions is None:
+            self._moldrawoptions = rdMolDraw2D.MolDraw2DSVG(300, 300).drawOptions()
+            self._moldrawoptions.prepareMolsBeforeDrawing = True
+            self._moldrawoptions.addStereoAnnotation = True
+            self._moldrawoptions.unspecifiedStereoIsUnknown = False
+            self._moldrawoptions.fixedBondLength = 25
+        else:
+            self._moldrawoptions = moldrawoptions
+
         # Bind signales to slots for automatic actions
         self.molChanged.connect(self.sanitize_draw)
         self.selectionChanged.connect(self.draw)
@@ -76,6 +86,25 @@ def darkmode(self, value: bool):
         self._darkmode = bool(value)
         self.draw()
 
+    @property
+    def moldrawoptions(self):
+        """Returns the current drawing options.
+        If settings aremanipulated directly, a drawSettingsChanged signal is not emitted,
+        consider using setDrawOption instead."""
+        return self._moldrawoptions
+
+    @moldrawoptions.setter
+    def moldrawoptions(self, value):
+        self._moldrawoptions = value
+        self.drawSettingsChanged.emit()
+
+    def getDrawOption(self, attribute):
+        return getattr(self._moldrawoptions, attribute)
+
+    def setDrawOption(self, attribute, value):
+        setattr(self._moldrawoptions, attribute, value)
+        self.drawSettingsChanged.emit()
+
     # Getter and setter for mol
     molChanged = QtCore.Signal(name="molChanged")
 
@@ -309,13 +338,15 @@ def getMolSvg(self):
         if self._drawmol is not None:
             # Chiral tags on R/S
             # chiraltags = Chem.FindMolChiralCenters(self._drawmol)
+            self.drawer.SetDrawOptions(self._moldrawoptions)
             opts = self.drawer.drawOptions()
             if self._darkmode:
                 rdMolDraw2D.SetDarkMode(opts)
             if (not self.molecule_sanitizable) and self.unsanitizable_background_colour:
                 opts.setBackgroundColour(self.unsanitizable_background_colour)
-            opts.prepareMolsBeforeDrawing = False
-            opts.addStereoAnnotation = True  # Show R/S and E/Z
+            # opts.prepareMolsBeforeDrawing = True
+            # opts.addStereoAnnotation = True  # Show R/S and E/Z
+            # opts.unspecifiedStereoIsUnknown = True  # Show wiggly bond at undefined stereo centre
             # for tag in chiraltags:
             #     idx = tag[0]
             #     opts.atomLabels[idx] = self._drawmol.GetAtomWithIdx(idx).GetSymbol() + ":" + tag[1]

rdeditor/rdEditor.py

@@ -33,6 +33,23 @@ def __init__(self, fileName=None, loglevel="WARNING"):
             [os.path.abspath(os.path.dirname(__file__)) + "/icon_themes/"]
         )
         self.loglevels = ["Critical", "Error", "Warning", "Info", "Debug", "Notset"]
+        # RDKit draw options, tooltip, default value is read from molViewWidget
+        self._drawopts_actions = [
+            (
+                "prepareMolsBeforeDrawing",
+                "Prepare molecules before drawing (i.e. fix stereochemistry and annotations)",
+            ),
+            (
+                "addStereoAnnotation",
+                "Add stereo annotation (R/S and E/Z)",
+            ),
+            (
+                "unspecifiedStereoIsUnknown",
+                "Show wiggly bond at potential undefined chiral stereo centres "
+                + "and cross bonds for undefined doublebonds",
+            ),
+        ]
+
         self.editor = MolEditWidget()
         self.chemEntityActionGroup = QtGui.QActionGroup(self, exclusive=True)
         self.ptable = PTable(self.chemEntityActionGroup)
@@ -133,6 +150,18 @@ def applySettings(self):
         self.editor.kekulize_on_cleanup = kekulize_on_cleanup
         self.cleanupSettingActions["kekulize_on_cleanup"].setChecked(kekulize_on_cleanup)
 
+        # Draw options
+        for key, statusTip in self._drawopts_actions:
+            viewer_value = self.editor.getDrawOption(key)
+            settings_value = self.settings.value(f"drawoptions/{key}", viewer_value, type=bool)
+            if settings_value != viewer_value:
+                self.editor.setDrawOption(key, settings_value)
+            self.drawOptionsActions[key].setChecked(settings_value)
+
+        if self.settings.contains("drawoptions/fixedBondLength"):
+            fixedBondLength = self.settings.value("drawoptions/fixedBondLength", 15, type=int)
+            self.editor.setDrawOption("fixedBondLength", fixedBondLength)
+
     # Function to setup status bar, central widget, menu bar, tool bar
     def SetupComponents(self):
         self.myStatusBar = QStatusBar()
@@ -218,6 +247,9 @@ def CreateMenus(self):
         self.cleanupMenu = self.settingsMenu.addMenu("Cleanup")
         for key, action in self.cleanupSettingActions.items():
             self.cleanupMenu.addAction(action)
+        self.drawOptionsMenu = self.settingsMenu.addMenu("Drawing Options")
+        for key, statusTip in self._drawopts_actions:
+            self.drawOptionsMenu.addAction(self.drawOptionsActions[key])
 
         # Help menu
         self.helpMenu.addAction(self.aboutAction)
@@ -452,6 +484,13 @@ def setLogLevel(self):
         self.settings.setValue("loglevel", loglevel)
         self.settings.sync()
 
+    def setDrawOption(self):
+        sender = self.sender()
+        option = sender.objectName()
+        self.editor.setDrawOption(option, sender.isChecked())
+        self.settings.setValue(f"drawoptions/{option}", sender.isChecked())
+        self.settings.sync()
+
     def setTheme(self):
         sender = self.sender()
         theme_name = sender.objectName()
@@ -914,6 +953,13 @@ def CreateActions(self):
             )
             self.loglevelActionGroup.addAction(self.loglevelactions[key])
 
+        self.drawOptionsActions = {}
+        for key, statusTip in self._drawopts_actions:
+            self.drawOptionsActions[key] = QAction(
+                key, self, statusTip=statusTip, triggered=self.setDrawOption, objectName=key, checkable=True
+            )
+            # self.drawOptionsActionGroup.addAction(self.drawOptionsActions[key])
+
         self.openChemRxiv = QAction(
             QIcon.fromTheme("icons8-Exit"),
             "ChemRxiv Preprint",